src/apps/benchmark/scientific/ddg_benchmark.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <protocols/init.hh>
#include <core/import_pose/import_pose.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <sstream>
#include <cmath>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <core/chemical/ResidueType.hh>

Typedefs
typedef std::vector< Real >	ddGs
Functions
std::ostream &	writeYamlValue (std::ostream &S, std::string name, core::Real value)
std::ostream &	writeYamlValue (std::ostream &S, std::string name, bool value)
Real	sum (ddGs &scores_to_sum)
Real	average (utility::vector1< Real > &scores_to_average)
Size	store_energies (ObjexxFCL::FArray2D< Real > &two_d_e_arrays, scoring::ScoreFunction &s, pose::Pose &p, Size next_index, Size size_to_expect)
Size	average_score_components (ObjexxFCL::FArray2D< Real > &scores_to_average, utility::vector1< Real > &averaged_scores)
Real	correlation_coefficient (utility::vector1< Real > sim, utility::vector1< Real > exp)
void	correlation (std::string ddg_out)
int	main (int argc, char *argv[])
Variables
static numeric::random::RandomGenerator	RG (946571)
static basic::Tracer	TR ("apps.pilot.yiliu.ddg")

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Detailed Description

Author:

Liz Kellogg ekellogg@u.washington.edu

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Typedef Documentation

typedef std::vector<Real> ddGs

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Function Documentation

Real average

(

utility::vector1< Real > &

scores_to_average

)

References color_pdb::i, and sum().

Referenced by main(), run_pep_prep(), and shift_angles().

Size average_score_components	(	ObjexxFCL::FArray2D< Real > &	scores_to_average,
		utility::vector1< Real > &	averaged_scores
	)

References color_pdb::i, ObjexxFCL::FArray2D< T >::l1(), ObjexxFCL::FArray2D< T >::l2(), ObjexxFCL::FArray2D< T >::u1(), and ObjexxFCL::FArray2D< T >::u2().

Referenced by main().

void correlation

(

std::string

ddg_out

)

References correlation_coefficient(), utility::io::oc::cout, basic::options::OptionKeys::ddg::ddg, basic::Tracer::Error, ObjexxFCL::getline(), basic::options::OptionKeys::ddg::mut, color_pdb::res, TR, writeYamlValue(), and revert_app::wt.

Referenced by main().

Real correlation_coefficient	(	utility::vector1< Real >	sim,
		utility::vector1< Real >	exp
	)

References utility::options::OptionKeys::options::exit, color_pdb::i, TR, and rosetta_py::utility::rankorder::x.

Referenced by correlation().

int main	(	int	argc,
		char *	argv[]
	)

References average(), average_score_components(), begin, correlation(), utility::io::oc::cout, basic::options::OptionKeys::ddg::debug_output, basic::options::OptionKeys::ddg::dump_pdbs, utility::options::OptionKeys::options::exit, ObjexxFCL::fmt::F(), utility::filename(), color_pdb::i, basic::options::OptionKeys::in::in, src::init(), basic::options::OptionKeys::ddg::iterations, get_pdb::line, basic::options::OptionKeys::casp::num_iterations, basic::options::OptionKeys::out::file::o, option, options, basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::loops::output_pdb, basic::options::OptionKeys::in::path::pdb, out::path::pdb(), PyMOL_demo::pose, NetLink::r, get_pdb::resnum, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), store_energies(), sum(), and basic::options::OptionKeys::casp::weight_file.

Size store_energies	(	ObjexxFCL::FArray2D< Real > &	two_d_e_arrays,
		scoring::ScoreFunction &	s,
		pose::Pose &	p,
		Size	next_index,
		Size	size_to_expect
	)

References begin, ObjexxFCL::FArray2D< T >::dimension(), end, color_pdb::i, and basic::options::OptionKeys::in::file::s.

Referenced by main().

Real sum

(

ddGs &

scores_to_sum

)

References color_pdb::i.

Referenced by average(), ObjexxFCL::dot(), ObjexxFCL::dot_product(), numeric::statistics::errf(), main(), ObjexxFCL::FArray2< double >::operator*=(), ObjexxFCL::FArray2< double >::right_multiply_by_transpose(), and statistics().

std::ostream& writeYamlValue	(	std::ostream &	S,
		std::string	name,
		core::Real	value
	)

Referenced by correlation(), and statistics().

std::ostream& writeYamlValue	(	std::ostream &	S,
		std::string	name,
		bool	value
	)

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Variable Documentation

numeric::random::RandomGenerator RG(946571) [static]

Referenced by basic::setup_tag2string().

basic::Tracer TR("apps.pilot.yiliu.ddg") [static]